How to Amend a PBD file for NAMD

From: Zeinab Emami (
Date: Wed Oct 01 2014 - 09:27:15 CDT

Dear Namd-list Members,

I face a problem regularly. When I use a PBD file obtained from internet,
NAMD cannot read it an I get this error while producing the autopsf psf

"Need to have at least one atom in your selection!"

I know the atom names and types and charges should be modified, though when
I tried to do it manually for a PDB file, I failed. I am wondering if
there is any automatic way to repair such a raw PDB file?

Thank you in advance and Best,

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:54 CST